Repeated sequences removal

The extracellular domain of cadherins consists of a variable number of a repeated sequence of about 110 amino acids. This sequence is termed the cadherin repeat and resembles in overall structure, but not in sequence, the Ig like domains. The cadherin repeat is the characteristic motive common to all members of the cadherin superfamily. Classical and desmosomal cadherins contain five cadherin repeats, but as many as 34 repeats have been found in the FAT cadherin (see below). Cadherins are calcium-dependent cell adhesion molecules, which means that removal of Ca2+, e.g., by chelating agents such as EDTA, leads to loss of cadherin function. The Ca2+-binding pockets are made up of amino acids from two consecutive cadherin repeats, which form a characteristic tertiary structure to coordinate a single Ca2+ion [1]. 

Figure 6. Probability density functions of the skews Sta ( ) and Sac ( ) values computed from the intronic sequences of the 14,854 intron-containing genes after removing repeated sequences, (a) Sense genes (b) antisense genes.

Once a sequence amplification event occurs, the nature of any selection on the copies is important. In many (or even most) cases, it appears that the majority of repeated DNA sequences represent pseudogenes, which mutate at a neutral rate of evolution.8 Along with amplification dynamics, the possible removal of repeated sequences must also be considered. Removal does not seem to play a major role with the interspersed repeated DNA elements,8,29 30 but it is likely to be important in tandemly repeated satellite elements. Other mechanisms might also alter evolution of parts of a repeated DNA sequence. For instance, human Alu family copies are initially rich in CpG dinucleotides. These sites appear to be approximately 10-fold more subject to mutation than other sites in the genome,19,31... 

AGTAGTAGTAGTAGT... ), etc. Due to polymerase slip (a.k.a. polymerase chatter), during DNA replication there is a slight chance these repeat sequences may become altered copies of the repeat unit can be created or removed. Consequently, the exact number of repeat units may differ between unrelated individuals. Considering all the known microsatellite markers, no two individuals are identical. This is the basis for forensic DNA identification and for testing of familial relationships (e.g., paternity testing). 

A crucial aspect of virtually all DNA-DNA hybridization studies is that they involve only so-called single-copy DNA (scDNA) or "unique DNA. Total genomic DNA is made single-stranded by heating and then allowed to reassociate into duplex DNA after cooling. Repeated copies of DNA sequences re-anneal faster than single-copy sequences due to their higher concentration in the solution. Thus, under controlled conditions and time, it is possible to remove excess copies of repeated sequences. 

An important point in understanding such experiments is that repeat sequences of DNA are not totally removed. All sequences are in molar ratio. This is because after excess copies of repeat sequences have reassociated, their dynamics of reassociation are similar to truly unique sequences. Thus no information is lost by discarding repetitive sequences, just redundant information due to repetition is discarded. 

Sometimes a complete metabolic pathway involves repeating a series of reactions several times over. Thus, the oxidation of fatty acids (section 5.5.2) proceeds by the sequential removal of two-carbon units. The removal of each two-carbon unit involves a repeated sequence of four reactions, and the end-product of each loop of the pathway is a fatty acid that is two carbons shorter than the one that entered the loop. It then undergoes the same sequence of reactions. This is shown in cartoon form in Figure 2.19. 

In naturally fractured formations, an additional damage mechanism is the loss of whole mud deep into the formation. This form of damage is very difficult to remove entirely. Such damage may require hydraulic fracturing or repeated sequences of stimulation fluid injection and production, which is not always possible. 

The resulting oligonucleotide is often of surprising purity as judged by analytic HPLC or electrophoresis, and up to 30 mg of a deoxyeicosanucleotide (20-base DNA) can be routinely obtained. Nevertheless small amounts of short sequences, resulting from capping and from base-catalysed hydrolysis, must always be removed by quick gel filtration, repeated ethanol precipitation from water (desalting), reverse-phase HPLC, gel electrophoresis, and other standard methods. 

---